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- PDB-1l8w: Crystal Structure of Lyme Disease Variable Surface Antigen VlsE o... -

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Basic information

Entry
Database: PDB / ID: 1l8w
TitleCrystal Structure of Lyme Disease Variable Surface Antigen VlsE of Borrelia burgdorferi
ComponentsVlsE1
KeywordsIMMUNE SYSTEM / Variable Surface Protein / VMP-like sequence
Function / homologyBorrelia lipoprotein / Borrelia lipoprotein / cell outer membrane / Variable large protein
Function and homology information
Biological speciesBorreliella burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsEicken, C. / Sharma, V. / Klabunde, T. / Lawrenz, M.B. / Hardham, J.M. / Norris, S.J. / Sacchettini, J.C.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Crystal structure of Lyme disease variable surface antigen VlsE of Borrelia burgdorferi.
Authors: Eicken, C. / Sharma, V. / Klabunde, T. / Lawrenz, M.B. / Hardham, J.M. / Norris, S.J. / Sacchettini, J.C.
History
DepositionMar 21, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Database references / Derived calculations ...Database references / Derived calculations / Source and taxonomy / Structure summary
Category: entity_name_com / entity_src_gen ...entity_name_com / entity_src_gen / pdbx_struct_mod_residue / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity_name_com.name / _entity_src_gen.pdbx_beg_seq_num ..._entity_name_com.name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _pdbx_struct_mod_residue.details / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Remark 300BIOMOLECULE: 1, 2, 3, 4 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF ...BIOMOLECULE: 1, 2, 3, 4 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). THE BIOLOGICAL ASSEMBLY IS ASSUMED TO BE A MONOMER. THE ASYMMETRIC UNIT CONTAINS 4 MONOMERS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VlsE1
B: VlsE1
C: VlsE1
D: VlsE1


Theoretical massNumber of molelcules
Total (without water)141,0974
Polymers141,0974
Non-polymers00
Water18,1951010
1
A: VlsE1


Theoretical massNumber of molelcules
Total (without water)35,2741
Polymers35,2741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: VlsE1


Theoretical massNumber of molelcules
Total (without water)35,2741
Polymers35,2741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: VlsE1


Theoretical massNumber of molelcules
Total (without water)35,2741
Polymers35,2741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: VlsE1


Theoretical massNumber of molelcules
Total (without water)35,2741
Polymers35,2741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
B: VlsE1
D: VlsE1


Theoretical massNumber of molelcules
Total (without water)70,5492
Polymers70,5492
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-22 kcal/mol
Surface area22690 Å2
MethodPISA
6
A: VlsE1
C: VlsE1


Theoretical massNumber of molelcules
Total (without water)70,5492
Polymers70,5492
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-15 kcal/mol
Surface area20950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.171, 59.178, 116.149
Angle α, β, γ (deg.)90.00, 104.58, 90.00
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11A-1045-

HOH

21A-2020-

HOH

31A-2666-

HOH

41B-1225-

HOH

51B-2068-

HOH

61B-2342-

HOH

71D-1231-

HOH

DetailsThe biological assembly is assumed to be a monomer. The asymmetric unit contains 4 monomers.

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Components

#1: Protein
VlsE1 / Variable large protein


Mass: 35274.266 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borreliella burgdorferi (Lyme disease spirochete)
Genus: Borrelia / Gene: vlsE / Production host: Escherichia coli (E. coli) / References: UniProt: O06878
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1010 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.72 % / Description: final refinement against 0.9797 data
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 1500, Hepes, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
pH: 8 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mMTris11pH8.0
215 %(w/v)PEG150011
310-15 mg/mlprotein11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.9611,0.9797,0.9800
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 3, 2000
RadiationMonochromator: CARS-design Si(111) double-bounce / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.96111
20.97971
30.981
ReflectionResolution: 2.3→90 Å / Num. all: 90139 / Num. obs: 90139 / % possible obs: 92.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0.5 / Biso Wilson estimate: 23 Å2 / Rsym value: 0.057
Reflection shellResolution: 2.3→2.38 Å / Rsym value: 0.138 / % possible all: 75
Reflection
*PLUS
Lowest resolution: 90 Å / Rmerge(I) obs: 0.051
Reflection shell
*PLUS
Highest resolution: 2.3 Å / % possible obs: 75 % / Rmerge(I) obs: 0.138

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.3→82.43 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 186825.69 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.291 4897 10.1 %RANDOM
Rwork0.216 ---
all-48581 --
obs-48581 96.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 84.1577 Å2 / ksol: 0.363979 e/Å3
Displacement parametersBiso mean: 41.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å20 Å2-11.7 Å2
2---7.08 Å20 Å2
3---7.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.3→82.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7984 0 0 1010 8994
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d18.7
X-RAY DIFFRACTIONc_improper_angle_d0.65
X-RAY DIFFRACTIONc_mcbond_it1.391.5
X-RAY DIFFRACTIONc_mcangle_it2.272
X-RAY DIFFRACTIONc_scbond_it2.12
X-RAY DIFFRACTIONc_scangle_it32.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.319 768 10.4 %
Rwork0.257 6636 -
obs--89.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Num. reflection obs: 41131 / Num. reflection Rfree: 4597 / Rfactor obs: 0.204 / Rfactor Rfree: 0.282 / Rfactor Rwork: 0.204
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.08
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.65
LS refinement shell
*PLUS
Rfactor Rfree: 0.319 / Rfactor Rwork: 0.257 / Rfactor obs: 0.257

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